The report contains some interesting insights on how that relationship may evolve and it will doubtless color any future discussions on the accession of the EU to the European Convention on Human Rights. He does not seem to think much of the EU Charter of Fundamental Rights and considers that EU accession to the European Convention on Human Rights is inevitable:
I believe that there is no alternative to the draft Treaty establishing a Constitution for Europe. However, since EU accession to the ECHR is of fundamental importance for Europeans, and since all the member states are agreed on it, there is no reason why it should not go ahead as soon as possible. Taking an exceptional step, and already building an institutional bridge between the EU and the Council, will neither undermine nor subvert the draft Constitutional Treaty.
I therefore suggest that the Governments of the member states act under Article 48 of the Treaty on European Union [...], and submit to their parliaments, in protocol form, a decision paving the way for EU accession to the ECHR."
As for the future European Fundamental Rights Agency, he has this to say :
The European Fundamental Rights Agency (AEDF) is a sensitive issue in EU/Council of Europe relations. A lot has been said about the threat which this new institution might pose to unity of the European human rights protection system. The Council of Europe must remain the benchmark for human rights in Europe. [...]
This means that the future Agency must be strictly complementary to the Council of Europe’s human rights observation and monitoring instruments. It is essential that its mandate be limited to human rights issues which arise in connection with the implementation of Community law, i.e. strictly within the EU’s internal legal system. It may never be extended to general observation, using its own procedures and resources, of the human rights situation in Council of Europe member states.
The report ends with fifteen recommendations. Worth reading.